From dc5e3bd4a0cb8741f0dacb00dcdfe66b3c82b97e Mon Sep 17 00:00:00 2001
From: ibludau <isabell.bludau@gmail.com>
Date: Wed, 1 Sep 2021 18:06:31 +0200
Subject: [PATCH] CHORE clean nbs

---
 Workflow.ipynb         | 66 +++++++++++++++++-------------------------
 alphamap/_nbdev.py     | 18 ++++++------
 nbs/SequencePlot.ipynb | 40 ++++++++++++-------------
 3 files changed, 55 insertions(+), 69 deletions(-)

diff --git a/Workflow.ipynb b/Workflow.ipynb
index 4e37311..e8a4371 100644
--- a/Workflow.ipynb
+++ b/Workflow.ipynb
@@ -23,7 +23,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -32,7 +32,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -48,7 +48,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -57,7 +57,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -82,7 +82,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -91,7 +91,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -115,7 +115,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -124,7 +124,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -140,7 +140,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -150,7 +150,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -7638,7 +7638,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -7657,7 +7657,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -7667,7 +7667,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -15730,7 +15730,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -15747,7 +15747,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -15756,7 +15756,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -20473,7 +20473,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -20490,7 +20490,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -20499,7 +20499,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -25976,7 +25976,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -25993,7 +25993,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -26002,10 +26002,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
-   "metadata": {
-    "scrolled": false
-   },
+   "execution_count": null,
+   "metadata": {},
    "outputs": [
     {
      "data": {
@@ -29382,7 +29380,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -29399,7 +29397,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -29408,7 +29406,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -36705,18 +36703,6 @@
    "display_name": "Python 3",
    "language": "python",
    "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.0"
   }
  },
  "nbformat": 4,
diff --git a/alphamap/_nbdev.py b/alphamap/_nbdev.py
index 97f7afa..34a0188 100644
--- a/alphamap/_nbdev.py
+++ b/alphamap/_nbdev.py
@@ -13,17 +13,12 @@
          "convert_fragpipe_mq_mod": "Importing.ipynb",
          "import_fragpipe_data": "Importing.ipynb",
          "import_data": "Importing.ipynb",
-         "all_organisms": "organisms_data.ipynb",
-         "import_fasta": "organisms_data.ipynb",
-         "import_uniprot_annotation": "organisms_data.ipynb",
          "expand_protein_ids": "Preprocessing.ipynb",
          "pep_position_helper": "Preprocessing.ipynb",
          "get_peptide_position": "Preprocessing.ipynb",
          "get_ptm_sites": "Preprocessing.ipynb",
          "get_modifications": "Preprocessing.ipynb",
          "format_input_data": "Preprocessing.ipynb",
-         "protease_dict": "proteolytic_cleavage.ipynb",
-         "get_cleavage_sites": "proteolytic_cleavage.ipynb",
          "format_uniprot_annotation": "SequencePlot.ipynb",
          "ptm_shape_dict": "SequencePlot.ipynb",
          "get_plot_data": "SequencePlot.ipynb",
@@ -38,14 +33,19 @@
          "resolve_unclear_position": "Uniprot_integration.ipynb",
          "extract_positions": "Uniprot_integration.ipynb",
          "preprocess_uniprot": "Uniprot_integration.ipynb",
-         "uniprot_feature_dict": "Uniprot_integration.ipynb"}
+         "uniprot_feature_dict": "Uniprot_integration.ipynb",
+         "all_organisms": "organisms_data.ipynb",
+         "import_fasta": "organisms_data.ipynb",
+         "import_uniprot_annotation": "organisms_data.ipynb",
+         "protease_dict": "proteolytic_cleavage.ipynb",
+         "get_cleavage_sites": "proteolytic_cleavage.ipynb"}
 
 modules = ["importing.py",
-           "organisms_data.py",
            "preprocessing.py",
-           "proteolytic_cleavage.py",
            "sequenceplot.py",
-           "uniprot_integration.py"]
+           "uniprot_integration.py",
+           "organisms_data.py",
+           "proteolytic_cleavage.py"]
 
 doc_url = "https://mannlabs.github.io/alphamap/"
 
diff --git a/nbs/SequencePlot.ipynb b/nbs/SequencePlot.ipynb
index 5855b6e..57de681 100644
--- a/nbs/SequencePlot.ipynb
+++ b/nbs/SequencePlot.ipynb
@@ -78,7 +78,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/opt/anaconda3/envs/alphamap/lib/python3.8/site-packages/IPython/core/interactiveshell.py:3357: DtypeWarning: Columns (2) have mixed types.Specify dtype option on import or set low_memory=False.\n",
+      "/opt/anaconda3/envs/alphamap/lib/python3.8/site-packages/IPython/core/interactiveshell.py:3361: DtypeWarning: Columns (2) have mixed types.Specify dtype option on import or set low_memory=False.\n",
       "  if (await self.run_code(code, result,  async_=asy)):\n"
      ]
     }
@@ -3698,9 +3698,9 @@
        }
       },
       "text/html": [
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+      "/opt/anaconda3/envs/alphamap/lib/python3.8/site-packages/IPython/core/interactiveshell.py:3361: DtypeWarning:\n",
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        "                            \n",
-       "var gd = document.getElementById('395bbc2a-68d8-49cd-a00c-a71e5794b7c0');\n",
+       "var gd = document.getElementById('d89e72b1-6606-4a5d-8f2d-563f86688934');\n",
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        "        var display = window.getComputedStyle(gd).display;\n",
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@@ -30106,7 +30106,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python [conda env:alphamap]",
+   "display_name": "Python [conda env:alphamap] *",
    "language": "python",
    "name": "conda-env-alphamap-py"
   }